diff RPKM_saturation.xml @ 63:27e16a30667a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de

--- a/RPKM_saturation.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/RPKM_saturation.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -4,13 +4,9 @@
         <import>rseqc_macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
-
-    <expand macro="requirements" />
-
-    <expand macro="stdio" />
-
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <version_command><![CDATA[RPKM_saturation.py --version]]></version_command>
-
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         RPKM_saturation.py -i 'input.${extension}' -o output -r '${refgene}'
@@ -36,53 +32,49 @@
         -l ${percentileFloor} -u ${percentileCeiling} -s ${percentileStep} -c ${rpkmCutoff}
         --mapq $mapq
     ]]></command>
-
     <inputs>
-        <expand macro="bam_sam_param" />
-        <expand macro="refgene_param" />
-        <expand macro="strand_type_param" />
+        <expand macro="bam_sam_param"/>
+        <expand macro="refgene_param"/>
+        <expand macro="strand_type_param"/>
         <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/>
-        <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)" />
-        <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)" />
-        <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)" />
-        <expand macro="mapq_param" />
-        <expand macro="rscript_output_param" />
+        <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)"/>
+        <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)"/>
+        <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)"/>
+        <expand macro="mapq_param"/>
+        <expand macro="rscript_output_param"/>
     </inputs>
-
     <outputs>
-        <expand macro="pdf_output_data" filename="output.saturation.pdf" />
+        <expand macro="pdf_output_data" filename="output.saturation.pdf"/>
         <data format="tabular" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string}: RPKM"/>
         <data format="tabular" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string}: raw count"/>
-        <expand macro="rscript_output_data" filename="output.saturation.r" />
+        <expand macro="rscript_output_data" filename="output.saturation.r"/>
     </outputs>
-
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
             <param name="refgene" value="hg19.HouseKeepingGenes_30.bed"/>
-            <param name="rscript_output" value="true" />
+            <param name="rscript_output" value="true"/>
             <output name="outputxls">
-              <assert_contents>
-                <has_n_columns n="26" />
-                <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" />
-              </assert_contents>
+                <assert_contents>
+                    <has_n_columns n="26"/>
+                    <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*"/>
+                </assert_contents>
             </output>
             <output name="outputrawxls">
-              <assert_contents>
-                <has_n_columns n="26" />
-                <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" />
-              </assert_contents>
+                <assert_contents>
+                    <has_n_columns n="26"/>
+                    <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*"/>
+                </assert_contents>
             </output>
             <output name="outputr">
-              <assert_contents>
-                <has_text text="pdf('output.saturation.pdf')" />
-                <has_line_matching expression="S5=c\(\d+\.\d+\)" />
-              </assert_contents>
+                <assert_contents>
+                    <has_text text="pdf('output.saturation.pdf')"/>
+                    <has_line_matching expression="S5=c\(\d+\.\d+\)"/>
+                </assert_contents>
             </output>
-            <output name="outputpdf" file="output.saturation.pdf" compare="sim_size" />
+            <output name="outputpdf" file="output.saturation.pdf" compare="sim_size"/>
         </test>
     </tests>
-
     <help><![CDATA[
 RPKM_saturation.py
 ++++++++++++++++++
@@ -163,7 +155,5 @@
 
 ]]>
     </help>
-
-    <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>